AlphaFold background
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
Single mutation to be modeled I recently had an interesting challenge, that of creating a molecular model of a protein expressed from a gene with a newly identified single amino acid mutation. I (wrongly) assumed that it would be a “simple” 3D homology modeling problem, solved by common methods. It turns out that the protein …
SUMMARY: Check calendar for Free "R" and "Python" workshops (Steenbock Library.) "Introduction to R with RStudio," "Data Wrangling in R" (SSCC - Social Science Computing Cooperative.) "Automating Tasks with the Unix Shell," "Data Management with SQL," "R: introduction / visualization / reports" (Software Carpentry through UW-Madison Data Science (fees apply).)
Default preferences I enjoy using R and RStudio, but I am always weary of upgrading R because that usually leads to some issue(s). The most recent was a bit long for me to diagnose, even though in retrospect it is a simple change in default preference, namely changing the default setting default.stringsAsFactors() from TRUE in …
PowerShell One day I discovered that there was a Windows App called “PowerShell” while searching on my Windows 10 installation. I did not pay much attention to it even if I stumbled upon it a few times since. It seems that the early versions were present already in Windows 7, so in that sense it …
(Last edit: April 11, 2023) Summary How to deal with many Excel files If I had had the information I was looking for within a single Excel spreadsheet I would not have found csvkit because I would simply have copied the column containing the data I wanted, in that case a list of email. But …
SUMMARY: Check calendar for Free "R" and "Python" workshops (Steenbock Library.) "Introduction to R with RStudio," "Data Wrangling in R" (SSCC - Social Science Computing Cooperative.) "Automating Tasks with the Unix Shell," "Data Management with SQL," "Introduction to Docker" (Software Carpentry through UW-Madison Data Science (fees apply).)
Does data analysis feel like the impossible job of "catching the moon?" Fortunately R and RStudio are great tools to analyze data and illustrate conclusions, while at the same time keeping records and create "live" documents that can be updated with "just one click." The material is written in a way that is conducive to "learn by doing" following demonstrations and examples. All code and all necessary materials and files are available and therefore it is possible to learn and acquire proficiency on one's own with this course content.
June 26, 2020. I have added a new entry under the “Tutorials” menu for “bioinformatics” to provide a place for tutorials that are more than just about one subject. “bioinformatics is the science of collecting and analyzing complex biochemical and biological information using computers.” It may provide the tools to “look under the hood” …
...provides a wonderfully well done, easy to understand set of small tutorials, with exercises, each with an accompanying video that should make it easier for beginners that want to learn Unix command line / bash.... To make is faster to navigate the lessons and videos I have combined both into a simple table...